FONDAP CENTERS OF EXCELLENCE IN RESEARCH PROGRAM FINAL FIVE YEAR REPORT 2011-2015 Center for Genome Regulation (CGR) 1 FONDAP CENTERS OF RESEARCH PROGRAM FINAL REPORT FIRST FIVE-YEAR PERIOD FONDAP CENTER FOR GENOME REGULATION (CGR) Guidelines: ​ The report should be written following the format specified hereafter. Both a printed (report and excel spreadsheets) and an electronic version must be sent to the following address: PROGRAMA CENTROS DE EXCELENCIA FONDAP CONICYT Moneda 1375, Floor 9 Santiago E-mail: [email protected] ​ Phone: (56 – 2) 2435 43 27 For future inquiries, please contact: María Eugenia Camelio FONDAP Program Interim Director E-mail: [email protected] 2 I. PRESENTATION PERIOD COVERED: From: January 2011 To: June 2015 ​ NAME OF THE CENTER CODE FONDAP Center for Genome Regulation 15 09 00 07 DIRECTOR OF THE CENTER E-MAIL SIGNATURE Dr. Miguel L Allende [email protected] DEPUTY DIRECTOR E-MAIL SIGNATURE [email protected] Dr. Martín Montecino SPONSORING INSTITUTION Universidad de Chile SPONSORING INSTITUTION E-MAIL SIGNATURE REPRESENTATIVE Prof. Víctor Cifuentes (Dean) [email protected] ASSOCIATED INSTITUTION(S) (if applicable) ​ Pontificia Universidad Católica de Chile, Universidad Andrés Bello CENTER WEBSITE ADDRESS www.genomacrg.cl DATE: 10/7/15 ​ 3 II. EXECUTIVE SUMMARY Five years ago, the FONDAP Center for Genome Regulation (CGR) set for itself a list of strategic and scientific objectives that would significantly change the landscape of Chilean genomic science and biological research. At the midpoint of the projected 10­year period in which these goals were to be accomplished, we can say that we are in the presence of a completely new scenario. The capacity for undertaking complex genome projects in the country has indeed advanced to the point of being on par with that of other nations and centers of similar scope. Training of investigators, mostly at the doctoral and postdoctoral levels, has generated sufficient expertise in the CGR to meet the challenges that we have faced successfully. The technological capacity required for the projects have accompanied our development, both in terms of sequencing capacity and computing power. We can declare with confidence, that we are now the reference center for genome projects in Chile, fulfilling our main strategic ​ goal. Scientifically, we were able to identify relevant biological problems that satisfied two important criteria: first, they address unanswered questions in fundamental biology with ramifications in evolution, genome architecture, gene regulation and epigenetics. Second, they involve organisms that are important to the country because of the significance of their biological heritage, the uniqueness of their environments and the special natural history they have led as species. We have complemented these studies with model or economically valuable organisms and with a landmark project on human genomics. All of the projects have advanced to the point of revealing interesting and novel features that will be of high impact, as is described below. Importantly, these Center projects were addressed with the input and active participation of all of the six Principal Investigators with the support of the Associate Investigators in specific instances. In this sense, it is noteworthy that CGR members have committed to give priority and to dedicate their main efforts towards the Center projects, a true measure of the impact of collective ­as opposed to individual­ funding. In other words, the funding for the CGR has generated new areas of research, inaccessible to lone researchers, and has spawned synergistic interactions between investigators of different backgrounds, justifying their grouping under one scientific umbrella institution. The impact of the CGR has been felt in other, perhaps more expected, ways. As has been predicted, training has been one of our strongest indicators. The number of postdocs, students and professionals that have worked at the CGR is in the hundreds, which attests to the attractiveness of the Center to young scientists from all over the world. This has been complemented with courses, workshops, conferences and our internal dissemination of the science carried out at the CGR, of which these young people have been the main beneficiaries. We have not forgotten our responsibility towards the nation and society and we have made substantial efforts to promote our science and to educate on the subjects of our expertise. Our investigators are all leaders in their own right and many of us have been involved in policy making, in government and in the private sector, impacts that are often neglected to be mentioned in scientific evaluations. Finally, a measure of impact has to do with the generation of critical mass and the creation of new opportunities for Chilean science to develop. One of our strategic decisions has been to form a network of researchers that can use the expertise available at the CGR for their own independent projects. We have directly collaborated with numerous groups and scientists making possible that their projects advance far more robustly and efficiently. This “spillover” effect was also intended from the outset, as we were aware that our center offered the opportunity to disseminate an expertise and know how that many Chilean scientists were in need of. I will summarize the salient results and effects that the CGR has generated in the first five years of operation in the following paragraphs emphasizing the qualitative outcome of the project, considering that details on the products themselves will be forthcoming in the appropriate sections of the report. 4 Strategic achievements Of the few projects involving genomics carried out before 2010 in Chile, none had achieved results that could be considered to significantly improve the capacities or make resources widely available for work in this area. This was mostly due to the modest funding these projects received and their limited scope. The FONDAP award received by the CRG thus constitutes a turning point, since the project involved a critical mass of researchers from three different universities and funding that, for Chilean standards, was sufficient to generate an ambitious plan. Simultaneously ­and critically for the success of this endeavour­ two awards were given for projects in infrastructure: a next generation sequencing platform (later to become OMICs Solutions) and a very large computing facility (eventually, the NLHPC), funded by the CONICYT Program for Major Scientific Equipment. This fortuitous conjunction of events, allowed us to forgo the need for investing in equipment and to focus on the experimental aspects of our project. Today, we can say that, in our country, we have all that is needed for research in advanced genome science: a Center with the capacity to identify relevant questions and the know how for addressing them, the latest sequencing technology, and the most advanced computing power in the region. This fulfills our first, and most important, strategic goal. As is the case with many Centers of Excellence in the country, the CGR is made up of investigators that are geographically and institutionally separated. Thus, there is no physical building or facility that groups us, a fact that we have sought to compensate in different ways. As a second strategic goal, we had wished to ameliorate this problem and we have attempted to find a solution albeit without a positive result to this day. Nonetheless, we have still managed to forge an identity as a Center and to become visible to the national and international scientific community (the third strategic goal). We have been approached by colleagues for collaborative projects, by the press for opinion and commentary and by government institutions for assistance and policy making. Besides these measures of recognition, scientists have started to join the CRG based on its reputation, in addition to the usual mechanism of recruitment that has to do with the visibility of its scientists as individuals. Three young Chilean researchers that trained as postdocs abroad and that had achieved independence, have returned to the country and have started projects within the CGR. All three are now seeking positions in academia (one successfully as of this writing) but they were able to return to the country only because the CGR gave them space, funding and an appropriate atmosphere for their re­insertion. In addition, five of our own postdocs were able to obtain academic positions in Chilean universities. Of these eight starting young scientists, two have been incorporated as Associate Investigators of the CGR. We’ve also hosted numerous visiting professors and one sabbatical stay at the Center, all of which speaks to the attractiveness of the CGR for career development. Scientific achievements. ​ A major turning point in the history of the CGR was the appointment of an internal Scientific Advisory Committee that could guide us in identifying research directions that would be most fruitful with our resources and capacities. Reaching a definition of exactly what we should do as a Center was not easy and, admittedly, was not achieved until late in the second year of our funding period. The CGR could not simply be a “genomics center”, dedicated to genome sequencing for the sake of it. Our expertise and history has been in fundamental biological research in cell biology, molecular genetics and regulatory modeling. However, our backgrounds in different organisms (microbes, plants and animal systems) and approaches (metabolic networks, cell differentiation, developmental genetics, etc.) meant that it was not trivial to find common ground for a collective project. It is tempting, and is commonplace in centers without a clear focus, to continue along the research lines that have been successful previously, and which are likely to continue to produce a strong publication record. Our Advisory Committee was key in suggesting that we look for Center Projects, that involved at least the group of six PIs and ideally all of the AIs and that would make us stand out with a clear identity (not just as the sum of the parts).